CountOrthologs: Count Ortholog Genes in a Species

In shinyWGD: 'Shiny' Application for Whole Genome Duplication Analysis

Count Ortholog Genes in a Species

Description

This function counts ortholog genes in a given species based on input data.

Usage

CountOrthologs(atomic.df, species)

Arguments

atomic.df

A data frame containing information about ortholog genes. It should have the following columns: - multiplicon: The multiplicon identifier. - geneX: The gene identifier in speciesX. - speciesX: The species name for geneX. - listX: The chromosome or list identifier for geneX. - coordX: The coordinate information for geneX. - geneY: The gene identifier in speciesY. - speciesY: The species name for geneY. - listY: The chromosome or list identifier for geneY. - coordY: The coordinate information for geneY. - level: The orthology level. - num_anchors: The number of anchors. - is_real: A flag indicating if the data is real. - Ks: The Ks value.

species

The species for which ortholog gene counts should be computed.

Value

A data frame summarizing the counts of ortholog genes for each chromosome.

shinyWGD documentation built on April 4, 2025, 2:28 a.m.